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The main advantages of the high speed machine are small size and high power density. However, the high speed machine suffers from higher loss density and cooling difficulty due to small cooling area, especially the high frequency harmonic currents produced by the power conversion system increase the loss and temperature of high speed machine. The output high frequency AC power of the high speed PM generator needs to be converted into the AC power with constant frequency and voltage using AC/DC/AC converter. In order to reduce the current harmonics of high speed generator produced by the AC/DC rectifier, the structure and control strategy of a combined PWM inverter/active power filter (APF) are introduced in this paper. The converter is first utilized as a PWM inverter to drive the generator for the micro-turbine starting, and then operates as an APF during the normal power conversion. The relationship of capacity between active filter and compensation object is analyzed. The simulation results show the feasibility of the proposed design structure and control strategy.